3LY2

Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Water-soluble PDE4 inhibitors for the treatment of dry eye.

Govek, S.P.Oshiro, G.Anzola, J.V.Beauregard, C.Chen, J.Coyle, A.R.Gamache, D.A.Hellberg, M.R.Hsien, J.N.Lerch, J.M.Liao, J.C.Malecha, J.W.Staszewski, L.M.Thomas, D.J.Yanni, J.M.Noble, S.A.Shiau, A.K.

(2010) Bioorg Med Chem Lett 20: 2928-2932

  • DOI: https://doi.org/10.1016/j.bmcl.2010.03.023
  • Primary Citation of Related Structures:  
    3LY2

  • PubMed Abstract: 

    PDE4 inhibitors have the potential to alleviate the symptoms and underlying inflammation associated with dry eye. Disclosed herein is the development of a novel series of water-soluble PDE4 inhibitors. Our studies led to the discovery of coumarin 18, which is effective in a rabbit model of dry eye and a tear secretion test in rats.


  • Organizational Affiliation

    Kalypsys, Inc., 10420 Wateridge Circle, San Diego, CA 92121, United States. sgovek@san.rr.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A, B, C, D, E
A, B, C, D, E, F, G, H
357Homo sapiensMutation(s): 0 
Gene Names: DPDE4PDE4B
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
PHAROS:  Q07343
GTEx:  ENSG00000184588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z72
Query on Z72

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
I [auth A]
M [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
I [auth A],
M [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
8-(cyclopentyloxy)-4-[(3,5-dichloropyridin-4-yl)amino]-7-methoxy-2H-chromen-2-one
C20 H18 Cl2 N2 O4
YUTTWVBLGONANE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth A],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
GA [auth H]
J [auth A]
N [auth B]
AA [auth F],
DA [auth G],
GA [auth H],
J [auth A],
N [auth B],
R [auth C],
U [auth D],
X [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
HA [auth H]
K [auth A]
O [auth B]
BA [auth F],
EA [auth G],
HA [auth H],
K [auth A],
O [auth B],
S [auth C],
V [auth D],
Y [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Z72 PDBBind:  3LY2 IC50: 5 (nM) from 1 assay(s)
BindingDB:  3LY2 IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.796α = 90
b = 233.964β = 90
c = 165.258γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description